Forecasters said the region could see its wettest Christmas in years, increasing the risk of debris flows in areas scorched by wildfires in January.
Those burn scar zones have been stripped of vegetation by fire and are less able to absorb water.
On Wednesday, a falling tree killed a San Diego man, local news outlets reported. Further north, a Sacramento sheriff's deputy died in what appeared to be a weather-related crash.
San Bernardino County firefighters said they rescued people trapped in cars when mud and debris rushed down a road leading into Wrightwood, a resort town in the San Gabriel Mountains about 130km northeast of Los Angeles.
Firefighters also went door-to-door to check homes, and the area was under a shelter-in-place order, officials said.
Travis Guenther and his family were trapped in Lytle Creek after roaring waters washed out the only bridge in or out of their neighbourhood.
More than a dozen neighbours took shelter at a community centre or found hotel rooms.
"Everybody that left to go to work this morning is stuck," he said.
"Half the families are here, and half the families are on the other side of the creek."
Guenther said he had plenty of supplies and was coordinating with others in the community of about 280 people. Two nurses who live on his street offered to help anyone who may need medical attention.
Janice Quick, president of the Wrightwood Chamber of Commerce and a resident of the mountain town for 45 years, said a wildfire in 2024 left much of the terrain without tree coverage.
The storm also stranded Dillan Brown, his wife and 14-month-old daughter at a rented cabin in Wrightwood with almost no food and only enough diapers for about another day. Roads leading off the mountain and to a grocery store were blocked by rocks and debris, Brown said.
A resident posted a call for help in a Facebook group. In less than an hour, neighbours showed up with more than enough supplies to ride out the storm, including bread, vegetables, milk, nappies and wipes.
"I think we're a little sad and upset that we're not going to be home with our families," Brown said, but the "kindness shown is definitely an overwhelming feeling".
Residents around burn scar zones from the Airport Fire in Orange County were also ordered to evacuate.
Areas along the coast, including Malibu, were under a flood watch until Friday afternoon, and wind and flood advisories were issued for much of the Sacramento Valley and the San Francisco Bay Area.
Several roads, including a part of Interstate 5 near the Burbank Airport closed due to flooding.
The storms were the result of multiple atmospheric rivers carrying massive plumes of moisture from the tropics during one of the busiest travel weeks of the year.
Southern California typically gets 1.3 to 2.5 cm , of rain this time of year, but this week, many areas could see between 10 to 20cm with even more in the mountains, National Weather Service meteorologist Mike Wofford said.
Heavy snow and gusts created "near white-out conditions" in parts of the Sierra Nevada and made mountain pass travel treacherous.
Officials said there was a "considerable" avalanche risk around Lake Tahoe, and a winter storm warning was in effect until Friday morning.
Governor Gavin Newsom declared a state of emergency in six counties to allow state assistance in storm response.
The state deployed emergency resources and first responders to several coastal and Southern California counties, and the California National Guard was on standby.
The California Highway Patrol reported a seemingly weather-related crash south of Sacramento in which a Sacramento sheriff's deputy died.
James Caravallo, who was with the agency for 19 years, was apparently travelling at an unsafe speed, lost control on a wet road and crashed into a power pole, CHP Officer Michael Harper said.
